I guess the Pixies are "indie" compared to Madonna, but I think the last time you could accuse someone of hipsterism for preferring this song was 1995. It's been covered dozens of times and featured prominently in movies and TV shows.
1 Michael Jackson, "Billie Jean" vs. 16 Billy Bragg, "A New England"
I'm happy I learned about this Billy Bragg song from the bracket, but "Billie Jean" is a better pop song than "New England" is as a folk song.
8 Metallica, "Master of Puppets" vs. 9 David Bowie, "Modern Love"
My first exposure to heavy metal was the Simpsons episode with Spinal Tap, and my second was the feature-length mockumentary with Spinal Tap, whose name escapes me at the moment. As a result, it's always been difficult for me to ever take it seriously enough to genuinely enjoy it.
5 U2, "With or Without You" vs. 12 Def Leppard, "Photograph"
I can see why people turned against U2 style anthems, but these early ones still sound really good and not overplayed (even though they probably are).
4 The Police, "Every Breath You Take" vs. 13 Tom Petty and the Heartbreakers, "Free Fallin'"
6 Joy Division, "Love Will Tear Us Apart" vs. 11 Peter Gabriel, "In Your Eyes"
I have a theory, so far untested, that "Love Will Tear Us Apart" minus lyrics would work really well as a sitcom theme song. It would be one of those show intros where the actors' name appear on the screen concurrently with a short clip of them doing something archetypical, zany where appropriate. The title would be something like "A House Divided" or "One Big Family." These are just examples, obviously. If anyone would like to plan out the rest of the show I'd be happy to work together on a promo.
3 Queen and David Bowie, "Under Pressure" vs. 14 Dolly Parton, "9 to 5"
7 Guns n'Roses, "Sweet Child o'Mine" vs. 10 The B-52s, "Love Shack"
A professor at Minnesota has "Sweet Child o' Mine" as his ringtone, and even as a ringtone the opening is impressive.
2 Bon Jovi, "Livin' On A Prayer" vs. 15 Public Enemy, "Fight the Power"
Both good, "Fight the Power" feels more timeless while still sounding like something from the late 80s.